seqCNA

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see seqCNA.annot.

Copy number analysis of high-throughput sequencing cancer data


Bioconductor version: 3.9

Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization

Author: David Mosen-Ansorena

Maintainer: David Mosen-Ansorena <dmosen.gn at cicbiogune.es>

Citation (from within R, enter citation("seqCNA")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("seqCNA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("seqCNA")
seqCNA.pdf PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Genetics, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 3.0), GLAD(>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot(>= 0.99), methods
Imports
System Requirements samtools
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package seqCNA_1.30.0.tar.gz
Windows Binary seqCNA_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) seqCNA_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqCNA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqCNA
Bioc Package Browser https://code.bioconductor.org/browse/seqCNA/
Package Short Url https://bioconductor.org/packages/seqCNA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive